Design and construction of full-scale anaerobic digesters that co-digest manure with other substrates, such as food processing wastes, is challenging because of the large number of potential mixtures that can be fed to the digester. In this work we examine the relationship between results from bench-scale methods such as biochemical methane potential assays (BMPs) and sub pilot-scale reactors. The baseline feedstock for this study was beef manure from concrete feedlot pens (open and covered) in eastern Iowa. Additional co-digestion substrates tested were short-fiber cardboard, corn processing wastewater, enzyme processing wastewater and lagoon liquid. Substrates were characterized for total solids (TS), volatile solids (VS), chemical oxygen demand (COD), pH, alkalinity, and ammonia, after which BMPs were conducted on all substrates. Based on the BMP and anaerobic toxicity assay (ATA) results, a mixture was created and evaluated using BMPs and tested in 100-L sub pilot-scale reactors. This study showed that results from BMPs of feedstock co-digestion mixtures accurately estimated the range of methane produced from three 100-L, plug flow reactors.